We have developed a computer software package for Image MODeling (IMOD). The package includes several tools for analyzing and viewing three-dimensional biological image data. The software allows image data to be visualized as serial sections or serial tilts in a dynamic display that helps a viewer to comprehend 3-D organization. Volume data, represented as gray-scale values assigned to voxels, be sliced in any orientation, or subvolumes may be extracted for independent analysis. Graphic models of image data can be constructed, either by hand drawing of contours about features of interest or with the help of software tools that identify gray scale thresholds. The resulting graphic models may in turn be viewed by volume or contour surface rendering. Each graphic object is accessable for independent coloring, and the whole image can be analyzed for quantitative information.